MAST - Motif Alignment and Search Tool
MAST version 3.0 (Release date: 2001/03/01 11:41:04)
For further information on how to interpret these results or to get
a copy of the MAST software please access http://meme.sdsc.edu.
REFERENCE
If you use this program in your research, please cite:
Timothy L. Bailey and Michael Gribskov,
"Combining evidence using p-values: application to sequence homology
searches", Bioinformatics, 14(48-54), 1998.
DATABASE AND MOTIFS
DATABASE crp0.s (nucleotide)
Last updated on Thu Mar 1 08:28:36 2001
Database contains 18 sequences, 1890 residues
Scores for positive and reverse complement strands are combined.
MOTIFS meme.crp0.zoops.4.sunsparcsolaris.html (nucleotide)
MOTIF WIDTH BEST POSSIBLE MATCH
----- ----- -------------------
1 19 TGTGAGCGAGGTCACACTT
2 8 CGGCGGGG
3 10 GCATCGGGCG
PAIRWISE MOTIF CORRELATIONS:
MOTIF 1 2
----- ----- -----
2 0.33
3 0.29 0.40
No overly similar pairs (correlation > 0.60) found.
Random model letter frequencies (from non-redundant database):
A 0.281 C 0.222 G 0.229 T 0.267
SECTION I: HIGH-SCORING SEQUENCES
- Each of the following 18 sequences has E-value less than 10.
- The E-value of a sequence is the expected number of sequences
in a random database of the same size that would match the motifs as
well as the sequence does and is equal to the combined p-value of the
sequence times the number of sequences in the database.
- The combined p-value of a sequence measures the strength of the
match of the sequence to all the motifs and is calculated by
- finding the score of the single best match of each motif
to the sequence (best matches may overlap),
- calculating the sequence p-value of each score,
- forming the product of the p-values,
- taking the p-value of the product.
- The sequence p-value of a score is defined as the
probability of a random sequence of the same length containing
some match with as good or better a score.
- The score for the match of a position in a sequence to a motif
is computed by by summing the appropriate entry from each column of
the position-dependent scoring matrix that represents the motif.
- Sequences shorter than one or more of the motifs are skipped.
- The table is sorted by increasing E-value.
| Links | Sequence Name | Description | E-value | Length
|
|---|
|
| ce1cg
|
| 4.8e-05
| 105
|
|
| pbr322
|
| 0.00028
| 105
|
|
| male
|
| 0.0026
| 105
|
|
| ilv
|
| 0.0068
| 105
|
|
| ara
|
| 0.0087
| 105
|
|
| ompa
|
| 0.039
| 105
|
|
| lac
|
| 0.091
| 105
|
|
| crp
|
| 0.093
| 105
|
|
| uxu1
|
| 0.15
| 105
|
|
| malt
|
| 0.18
| 105
|
|
| gale
|
| 0.18
| 105
|
|
| bglr1
|
| 0.21
| 105
|
|
| deop2
|
| 0.27
| 105
|
|
| cya
|
| 0.28
| 105
|
|
| tnaa
|
| 0.35
| 105
|
|
| malk
|
| 0.71
| 105
|
|
| tdc
|
| 0.88
| 105
|
|
| trn9cat
|
| 1.2
| 105
|
SECTION II: MOTIF DIAGRAMS
- The ordering and spacing of all non-overlapping motif occurrences
are shown for each high-scoring sequence listed in Section I.
- A motif occurrence is defined as a position in the sequence whose
match to the motif has POSITION p-value less than 0.0001.
- The POSITION p-value of a match is the probability of
a single random subsequence of the length of the motif
scoring at least as well as the observed match.
- For each sequence, all motif occurrences are shown unless there
are overlaps. In that case, a motif occurrence is shown only if its
p-value is less than the product of the p-values of the other
(lower-numbered) motif occurrences that it overlaps.
- The table also shows the E-value of each sequence.
- Spacers and motif occurences are indicated by
- occurrence of motif `n' with p-value less than 0.0001.
A minus sign indicates that the occurrence is on the
reverse complement strand.
- Sequences longer than 1000 are not shown to scale and are indicated by thicker lines.
| Links | Name | Expect |    Motifs
|
|---|
|
| ce1cg
| 4.8e-05
|
|
|
| pbr322
| 0.00028
|
|
|
| male
| 0.0026
|
|
|
| ilv
| 0.0068
|
|
|
| ara
| 0.0087
|
|
|
| ompa
| 0.039
|
|
|
| lac
| 0.091
|
|
|
| crp
| 0.093
|
|
|
| uxu1
| 0.15
|
|
|
| malt
| 0.18
|
|
|
| gale
| 0.18
|
|
|
| bglr1
| 0.21
|
|
|
| deop2
| 0.27
|
|
|
| cya
| 0.28
|
|
|
| tnaa
| 0.35
|
|
|
| malk
| 0.71
|
|
|
| tdc
| 0.88
|
|
|
| trn9cat
| 1.2
|
|
| SCALE
|
|
|---|
SECTION III: ANNOTATED SEQUENCES
- The positions and p-values of the non-overlapping motif occurrences
are shown above the actual sequence for each of the high-scoring
sequences from Section I.
- A motif occurrence is defined as a position in the sequence whose
match to the motif has POSITION p-value less than 0.0001 as
defined in Section II.
- For each sequence, the first line specifies the name of the sequence.
- The second (and possibly more) lines give a description of the
sequence.
- Following the description line(s) is a line giving the length,
combined p-value, and E-value of the sequence as defined in Section I.
- The next line reproduces the motif diagram from Section II.
- The entire sequence is printed on the following lines.
- Motif occurrences are indicated directly above their positions in the
sequence on lines showing
- the motif number of the occurrence (a minus sign indicates that
the occurrence is on the reverse complement strand),
- the position p-value of the occurrence,
- the best possible match to the motif (or its reverse complement), and
- columns whose match to the motif has a positive score (indicated
by a plus sign).
ce1cg
LENGTH = 105 COMBINED P-VALUE = 2.67e-06 E-VALUE = 4.8e-05
DIAGRAM: 23-[+3]-30-[+1]-23
[+3] [+1]
5.1e-07 1.1e-06
GCATCGGGCG TGTGAGCGAGGT
++++++++++ ++++++++ ++
1 TAATGTTTGTGCTGGTTTTTGTGGCATCGGGCGAGAATAGCGCGTGGTGTGAAAGACTGTTTTTTTGATCGTTTT
CACACTT
++++ ++
76 CACAAAAATGGAAGTCCACAGTCTTGACAG
pbr322
LENGTH = 105 COMBINED P-VALUE = 1.54e-05 E-VALUE = 0.00028
DIAGRAM: 52-[-1]-21-[+3]-3
[-1]
4.7e-06
AAGTGTGACCTCGCTCACA
+++++++ + ++ ++++
1 CTGGCTTAACTATGCGGCATCAGAGCAGATTGTACTGAGAGTGCACCATATGCGGTGTGAAATACCGCACAGATG
[+3]
1.1e-06
GCATCGGGCG
++++++++++
76 CGTAAGGAGAAAATACCGCATCAGGCGCTC
male
LENGTH = 105 COMBINED P-VALUE = 1.45e-04 E-VALUE = 0.0026
DIAGRAM: 16-[+1]-5-[+2]-57
[+1] [+2]
3.6e-06 1.5e-05
TGTGAGCGAGGTCACACTT CGGCGGGG
+++ + +++ ++++++++ ++++++++
1 ACATTACCGCCAATTCTGTAACAGAGATCACACAAAGCGACGGTGGGGCGTAGGGGCAAGGAGGATGGAAAGAGG
ilv
LENGTH = 105 COMBINED P-VALUE = 3.79e-04 E-VALUE = 0.0068
DIAGRAM: 4-[+2]-29-[+1]-45
[+2] [+1]
7.0e-06 2.4e-05
CGGCGGGG TGTGAGCGAGGTCACACTT
++++++++ ++++++ ++ + ++ ++
1 GCTCCGGCGGGGTTTTTTGTTATCTGCAATTCAGTACAAAACGTGATCAACCCCTCAATTTTCCCTTTGCTGAAA
ara
LENGTH = 105 COMBINED P-VALUE = 4.84e-04 E-VALUE = 0.0087
DIAGRAM: 57-[+1]-29
[+1]
3.6e-08
TGTGAGCGAGGTCACACT
++++ ++++++++++++
1 GACAAAAACGCGTAACAAAAGTGTCTATAATCACGGCAGAAAAGTCCACATTGATTATTTGCACGGCGTCACACT
T
+
76 TTGCTATGCCATAGCATTTTTATCCATAAG
ompa
LENGTH = 105 COMBINED P-VALUE = 2.17e-03 E-VALUE = 0.039
DIAGRAM: 50-[+1]-36
[+1]
4.2e-07
TGTGAGCGAGGTCACACTT
+++ +++++++++++++
1 GCTGACAAAAAAGATTAAACATACCTTATACAAGACTTTTTTTTCATATGCCTGACGGAGTTCACACTTGTAAGT
lac
LENGTH = 105 COMBINED P-VALUE = 5.08e-03 E-VALUE = 0.091
DIAGRAM: 11-[+1]-75
[+1]
5.6e-06
TGTGAGCGAGGTCACACTT
++++++ ++ ++++ +++
1 AACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTG
crp
LENGTH = 105 COMBINED P-VALUE = 5.16e-03 E-VALUE = 0.093
DIAGRAM: 65-[+1]-21
[+1]
2.0e-06
TGTGAGCGAG
++ + ++++
1 CACAAAGCGAAAGCTATGCTAAAACAGTCAGGATGCTACAGTAATACATTGATGTACTGCATGTATGCAAAGGAC
GTCACACTT
++++++ ++
76 GTCACATTACCGTGCAGTACAGTTGATAGC
uxu1
LENGTH = 105 COMBINED P-VALUE = 8.28e-03 E-VALUE = 0.15
DIAGRAM: 19-[+1]-67
[+1]
1.9e-05
TGTGAGCGAGGTCACACTT
+++++++ ++++ ++ +++
1 CCCATGAGAGTGAAATTGTTGTGATGTGGTTAACCCAATTAGAATTCGGGATTGACATGTCTTACCAAAAGGTAG
malt
LENGTH = 105 COMBINED P-VALUE = 9.76e-03 E-VALUE = 0.18
DIAGRAM: 40-[-1]-46
[-1]
1.3e-06
AAGTGTGACCTCGCTCACA
++ ++++++ + + ++++
1 GATCAGCGTCGTTTTAGGTGAGTTGTTAATAAAGATTTGGAATTGTGACACAGTGCAAATTCAGACACATAAAAA
gale
LENGTH = 105 COMBINED P-VALUE = 1.01e-02 E-VALUE = 0.18
DIAGRAM: 44-[+1]-42
[+1]
1.3e-06
TGTGAGCGAGGTCACACTT
+++ ++ + +++++++++
1 GCGCATAAAAAACGGCTAAATTCTTGTGTAAACGATTCCACTAATTTATTCCATGTCACACTTTTCGCATCTTTG
bglr1
LENGTH = 105 COMBINED P-VALUE = 1.19e-02 E-VALUE = 0.21
DIAGRAM: 78-[+1]-8
[+1]
1.6e-06
TGTGAGCGAGGTCACACTT
+++++++ +++++ + ++
76 AACTGTGAGCATGGTCATATTTTTATCAAT
deop2
LENGTH = 105 COMBINED P-VALUE = 1.49e-02 E-VALUE = 0.27
DIAGRAM: 9-[+1]-31-[-1]-27
[+1] [-1]
2.7e-06 8.7e-06
TGTGAGCGAGGTCACACTT AAGTGTGACCTCGCTC
+++++ + ++ ++ ++ ++ ++ +++++ ++ +++
1 AGTGAATTATTTGAACCAGATCGCATTACAGTGATGCAAACTTGTAAGTAGATTTCCTTAATTGTGATGTGTATC
ACA
++
76 GAAGTGTGTTGCGGAGTAGATGTTAGAATA
cya
LENGTH = 105 COMBINED P-VALUE = 1.57e-02 E-VALUE = 0.28
DIAGRAM: 49-[-1]-37
[-1]
2.9e-06
AAGTGTGACCTCGCTCACA
+ ++++ ++ + ++++++
1 ACGGTGCTACACTTGTATGTAGCGCATCTTTCTTTACGGTCAATCAGCAAGGTGTTAAATTGATCACGTTTTAGA
tnaa
LENGTH = 105 COMBINED P-VALUE = 1.92e-02 E-VALUE = 0.35
DIAGRAM: 73-[+1]-13
[+
5.
TG
++
1 TTTTTTAAACATTAAAATTCTTACGTAATTTATAATCTTTAAAAAAAGCATTTAATATTGCTCCCCGAACGATTG
1]
1e-06
TGAGCGAGGTCACACTT
++++ + ++++++ ++
76 TGATTCGATTCACATTTAAACAATTTCAGA
malk
LENGTH = 105 COMBINED P-VALUE = 3.94e-02 E-VALUE = 0.71
DIAGRAM: 60-[-1]-26
[-1]
4.2e-05
AAGTGTGACCTCGCT
++ ++++ ++ +++
1 GGAGGAGGCGGGAGGATGAGAACACGGCTTCTGTGAACTAAACCGAGGTCATGTAAGGAATTTCGTGATGTTGCT
CACA
++
76 TGCAAAAATCGTGGCGATTTTATGTGCGCA
tdc
LENGTH = 105 COMBINED P-VALUE = 4.88e-02 E-VALUE = 0.88
DIAGRAM: 78-[+1]-8
[+1]
1.0e-05
TGTGAGCGAGGTCACACTT
++++ + + ++++ +++++
76 TAATTTGTGAGTGGTCGCACATATCCTGTT
trn9cat
LENGTH = 105 COMBINED P-VALUE = 6.71e-02 E-VALUE = 1.2
DIAGRAM: 83-[-1]-3
[-1]
2.4e-05
AAGTGTGACCTCGCTCACA
++ ++ +++++ ++++
76 TTTGGCGAAAATGAGACGTTGATCGGCACG
Debugging Information
CPU: nbcr2
Time 0.080000 secs.
mast meme.crp0.zoops.4.sunsparcsolaris.html -stdout
Button Help
Links to Entrez database at NCBI
Links to sequence scores (section I)
Links to motif diagrams (section II)
Links to sequence/motif annotated alignments (section III)
This information